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Detailed information for vg0805698451:

Variant ID: vg0805698451 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5698451
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CGGAGGGAGATGGAGCTCGGGGGCAGATGGCAGTGGGGGAGGGGGCAGGACGAAGAGGAGGAGAAGAGAGGGGAAGAGGAGTATACGGCCGCGGCGGCGG[C/T]
GGCGGCCAACGGCGGCGCCATGGGAGGAAGGTGAGGTCCGTGCACCTCCATATGCTTCTTCCTCCCTCGTCGCGGCTCGGCTTCGGATGACGAGCGGCGG

Reverse complement sequence

CCGCCGCTCGTCATCCGAAGCCGAGCCGCGACGAGGGAGGAAGAAGCATATGGAGGTGCACGGACCTCACCTTCCTCCCATGGCGCCGCCGTTGGCCGCC[G/A]
CCGCCGCCGCGGCCGTATACTCCTCTTCCCCTCTCTTCTCCTCCTCTTCGTCCTGCCCCCTCCCCCACTGCCATCTGCCCCCGAGCTCCATCTCCCTCCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.10% 21.60% 0.25% 0.00% NA
All Indica  2759 71.80% 28.00% 0.18% 0.00% NA
All Japonica  1512 99.40% 0.50% 0.07% 0.00% NA
Aus  269 21.60% 77.00% 1.49% 0.00% NA
Indica I  595 55.60% 43.70% 0.67% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 71.90% 28.10% 0.00% 0.00% NA
Indica Intermediate  786 72.10% 27.70% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805698451 C -> T LOC_Os08g09870.1 missense_variant ; p.Ala64Thr; MODERATE nonsynonymous_codon ; A64T Average:92.418; most accessible tissue: Zhenshan97 young leaf, score: 95.75 unknown unknown DELETERIOUS 0.00

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0805698451 C T -0.04 -0.04 -0.06 -0.04 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805698451 NA 9.51E-07 mr1038 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 NA 7.22E-07 mr1209 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 NA 9.46E-09 mr1389 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 NA 6.18E-08 mr1706 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 1.73E-06 NA mr1807 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 6.45E-07 6.41E-07 mr1954 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 NA 9.61E-07 mr1125_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0805698451 NA 2.62E-06 mr1553_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251